Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/dna_daq/stored-normals/reference-NA12878-downsampled-500k.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8f/8ee7221cb00667c7914a883215e2de/HCC1395_BL.recalibrated.bam
Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/af-only-gnomad.hg38.vcf.gz
Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/PON/pon_tnseq_42_curated_v4.vcf.gz
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/dna_daq/stored-normals/reference-NA12878-downsampled-500k.bam.bai
Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/af-only-gnomad.hg38.vcf.gz.tbi
Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/intervals/altera_padded_intervals/xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity_padded100bp.bed
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b3/1232fca46c2e38ae3017e6c0fa9168/.command.sh
Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/PON/pon_tnseq_42_curated_v4.vcf.gz.tbi
Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8f/8ee7221cb00667c7914a883215e2de/HCC1395_BL.recalibrated.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b3/1232fca46c2e38ae3017e6c0fa9168/.command.run
Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.dict
==> STAGING COMPLETE (14 inputs)
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 12 -r Homo_sapiens_assembly38.fasta -i reference-NA12878-downsampled-500k.bam -i HCC1395_BL.recalibrated.bam --interval xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity_padded100bp.bed --algo TNhaplotyper2 --tumor_sample HCC1395_BL --normal_sample reference-NA12878 --call_germline_sites --germline_vcf af-only-gnomad.hg38.vcf.gz --pon pon_tnseq_42_curated_v4.vcf.gz negative_somatic_control_1.tnseq.vcf.gz --algo OrientationBias --tumor_sample HCC1395_BL negative_somatic_control_1.tnseq.orientation_data.tsv --algo ContaminationModel --tumor_sample HCC1395_BL --normal_sample reference-NA12878 --vcf af-only-gnomad.hg38.vcf.gz --tumor_segments negative_somatic_control_1.tnseq.segments negative_somatic_control_1.tnseq.contamination_data.tsv
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:113711646, elapsed 0.7s, est remaining 12.8s, peak mem 143MB, user 6.7s, sys 0.5s, output queue size 4
progress 10% @chr2:3643344, elapsed 1.3s, est remaining 11.7s, peak mem 144MB, user 13.1s, sys 1.0s, output queue size 5
progress 15% @chr2:178606921, elapsed 2.0s, est remaining 11.1s, peak mem 145MB, user 20.0s, sys 1.4s, output queue size 12
progress 20% @chr3:57498400, elapsed 2.6s, est remaining 10.2s, peak mem 145MB, user 26.0s, sys 1.8s, output queue size 0
progress 25% @chr4:70631570, elapsed 3.2s, est remaining 9.6s, peak mem 146MB, user 32.8s, sys 2.3s, output queue size 3
progress 30% @chr5:135850325, elapsed 3.9s, est remaining 9.1s, peak mem 147MB, user 39.8s, sys 2.6s, output queue size 4
progress 35% @chr6:104957999, elapsed 4.5s, est remaining 8.3s, peak mem 147MB, user 45.9s, sys 3.0s, output queue size 2
progress 40% @chr7:106872437, elapsed 5.1s, est remaining 7.7s, peak mem 149MB, user 52.8s, sys 3.3s, output queue size 2
progress 45% @chr8:143821497, elapsed 5.8s, est remaining 7.1s, peak mem 150MB, user 59.5s, sys 3.7s, output queue size 1
progress 50% @chr10:21726144, elapsed 6.4s, est remaining 6.4s, peak mem 152MB, user 66.0s, sys 4.1s, output queue size 1
progress 55% @chr11:34132025, elapsed 7.1s, est remaining 5.8s, peak mem 152MB, user 72.5s, sys 4.4s, output queue size 1
progress 60% @chr12:12718707, elapsed 7.7s, est remaining 5.1s, peak mem 152MB, user 78.6s, sys 4.7s, output queue size 11
progress 65% @chr13:32078734, elapsed 8.3s, est remaining 4.5s, peak mem 153MB, user 85.2s, sys 5.2s, output queue size 10
progress 70% @chr15:35381722, elapsed 8.9s, est remaining 3.8s, peak mem 153MB, user 91.5s, sys 5.6s, output queue size 2
progress 75% @chr16:28494582, elapsed 9.6s, est remaining 3.2s, peak mem 153MB, user 98.1s, sys 5.9s, output queue size 0
progress 80% @chr17:40032956, elapsed 10.3s, est remaining 2.6s, peak mem 153MB, user 105.5s, sys 6.2s, output queue size 3
progress 85% @chr19:1805788, elapsed 10.9s, est remaining 1.9s, peak mem 154MB, user 112.2s, sys 6.6s, output queue size 2
progress 90% @chr19:54632916, elapsed 11.5s, est remaining 1.3s, peak mem 155MB, user 118.7s, sys 6.9s, output queue size 0
progress 95% @chr22:31897382, elapsed 13.0s, est remaining 0.7s, peak mem 324MB, user 133.9s, sys 7.4s, output queue size 10
progress 100% @chrY:12812730, elapsed 13.6s, est remaining 0.0s, peak mem 324MB, user 139.8s, sys 7.9s, output queue size 438
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
signature: 000606a6
features: 1f8bfbff fffa320b
extended: f1bf07ab 00407f5a
amd bits: 2c100800 00000121
brand: Intel(R) Xeon(R) Platinum 8375C CPU @ 2.90GHz
threads: 12 max 64
algo: TNhaplotyper2 OrientationBias ContaminationModel
license: sentieon:TNhaplotyper=12
input file size: 71721858 71692767
output file size: 46614
reads: 1501772
contig: 178193 intervals 76355618 bases
"assemble": 183 calls 0.417 user 0.000 sys 0.390 real
"assemble_addRead": 183 calls 0.000 user 0.000 sys 0.006 real
"assemble_buildGraph": 422 calls 0.196 user 0.000 sys 0.166 real
"assemble_computecigar": 264 calls 0.041 user 0.019 sys 0.070 real
"assemble_kg_build_calcsize": 422 calls 0.101 user 0.000 sys 0.086 real
"assemble_kg_build_clear": 573 calls 0.000 user 0.000 sys 0.006 real
"assemble_kg_build_prepare": 844 calls 0.121 user 0.000 sys 0.081 real
"assemble_kg_build_threading": 271 calls 0.095 user 0.000 sys 0.077 real
"assemble_kg_op1": 271 calls 0.050 user 0.000 sys 0.055 real
"assemble_kg_op2": 271 calls 0.000 user 0.000 sys 0.004 real
"assemble_kg_op3": 271 calls 0.000 user 0.000 sys 0.005 real
"assemble_sg_clean": 264 calls 0.020 user 0.000 sys 0.020 real
"assemble_sg_create": 264 calls 0.020 user 0.000 sys 0.030 real
"checkGraph": 183 calls 0.000 user 0.000 sys 0.000 real
"findHaplotype": 183 calls 0.041 user 0.019 sys 0.073 real
advance: 189104 calls 14.507 user 0.316 sys 18.522 real
assemble_region: 183 calls 0.458 user 0.029 sys 0.471 real
build_pileup: 70974 calls 0.352 user 0.001 sys 0.452 real
build_stats: 71688 calls 1.637 user 0.077 sys 2.182 real
build_variants: 142 calls 0.007 user 0.000 sys 0.001 real
calc: 128670 calls 2.246 user 0.020 sys 2.872 real
calc_region: 142 calls 2.287 user 0.012 sys 2.349 real
call_region: 142 calls 0.048 user 0.000 sys 0.036 real
clip_region: 325 calls 0.046 user 0.000 sys 0.026 real
done: 1 calls 0.438 user 0.000 sys 0.445 real
execute: 1 calls 0.009 user 0.001 sys 13.626 real
fetch: 743546 calls 0.784 user 0.072 sys 0.811 real
fetch_ref: 745688 calls 1.672 user 0.392 sys 2.740 real
fetch_region: 183 calls 0.000 user 0.000 sys 0.006 real
fetch_vcf: 189104 calls 43.686 user 0.746 sys 55.474 real
idle: 35 calls 0.002 user 0.031 sys 12.866 real
init: 1 calls 0.060 user 0.000 sys 0.059 real
pairhmm: 472 calls 3.245 user 0.010 sys 3.364 real
realign: 142 calls 0.278 user 0.000 sys 0.339 real
region: 367297 calls 2.765 user 0.048 sys 2.921 real
tracker: 367297 calls 0.366 user 0.081 sys 0.544 real
trim_region: 183 calls 0.000 user 0.000 sys 0.001 real
overall: 340738048 mem 155.235 user 10.371 sys 14.918 real